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Song M, Zhou Y, Zhao C, Song F, Hou Y. YHP: Y-chromosome Haplogroup Predictor for predicting male lineages based on Y-STRs. Forensic Sci Int 2024; 361:112113. [PMID: 38936202 DOI: 10.1016/j.forsciint.2024.112113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 05/24/2024] [Accepted: 06/16/2024] [Indexed: 06/29/2024]
Abstract
Human Y chromosome reflects the evolutionary process of males. Male lineage tracing by Y chromosome is of great use in evolutionary, forensic, and anthropological studies. Identifying the male lineage based on the specific distribution of Y haplogroups narrows down the investigation scope, which has been used in forensic scenarios. However, existing software aids in familial searching using Y-STRs (Y-chromosome short tandem repeats) to predict Y-SNP (Y-chromosome single nucleotide polymorphism) haplogroups, they often lack resolution. In this study, we developed YHP (Y Haplogroup Predictor), a novel software offering high-resolution haplogroup inference without requiring extensive Y-SNP sequencing. Leveraging existing datasets (219 haplogroups, 4064 samples in total), YHP predicts haplogroups with 0.923 accuracy under the highest haplogroup resolution, employing a random forest algorithm. YHP, available on Github (https://github.com/cissy123/YHP-Y-Haplogroup-Predictor-), facilitates high-resolution haplogroup prediction, haplotype mismatch analysis, and haplotype similarity comparison. Notably, it demonstrates efficacy in East Asian populations, benefiting from training data from eight distinct East Asian ethnic populations. Moreover, it enables seamless integration of additional training sets, extending its utility to diverse populations.
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Affiliation(s)
- Mengyuan Song
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China; Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Yuxiang Zhou
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Chenxi Zhao
- College of Computer Science, Sichuan University, Chengdu, China
| | - Feng Song
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China.
| | - Yiping Hou
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China.
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Fan H, Xu Y, Zhao Y, Feng K, Hong L, Zhao Q, Lu X, Shi M, Li H, Wang L, Wen S. Development and validation of YARN: A novel SE-400 MPS kit for East Asian paternal lineage analysis. Forensic Sci Int Genet 2024; 71:103029. [PMID: 38518712 DOI: 10.1016/j.fsigen.2024.103029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 02/12/2024] [Accepted: 03/03/2024] [Indexed: 03/24/2024]
Abstract
Y-chromosomal short tandem repeat polymorphisms (Y-STRs) and Y-chromosomal single nucleotide polymorphisms (Y-SNPs) are valuable genetic markers used in paternal lineage identification and population genetics. Currently, there is a lack of an effective panel that integrates Y-STRs and Y-SNPs for studying paternal lineages, particularly in East Asian populations. Hence, we developed a novel Y-chromosomal targeted panel called YARN (Y-chromosome Ancestry and Region Network) based on multiplex PCR and a single-end 400 massive parallel sequencing (MPS) strategy, consisting of 44 patrilineage Y-STRs and 260 evolutionary Y-SNPs. A total of 386 reactions were validated for the effectiveness and applicability of YARN according to SWGDAM validation guidelines, including sensitivity (with a minimum input gDNA of 0.125 ng), mixture identification (ranging from 1:1-1:10), PCR inhibitor testing (using substances such as 50 μM hematin, 100 μM hemoglobin, 100 μM humic acid, and 2.5 mM indigo dye), species specificity (successfully distinguishing humans from other animals), repeatability study (achieved 100% accuracy), and concordance study (with 99.91% accuracy for 1121 Y-STR alleles). Furthermore, we conducted a pilot study using YARN in a cohort of 484 Han Chinese males from Huaiji County, Zhaoqing City, Guangdong, China (GDZQHJ cohort). In this cohort, we identified 52 different Y-haplogroups and 73 different surnames. We found weak to moderate correlations between the Y-haplogroups, Chinese surnames, and geographical locations of the GDZQHJ cohort (with λ values ranging from 0.050 to 0.340). However, when we combined two different categories into a new independent variable, we observed stronger correlations (with λ values ranging from 0.617 to 0.754). Overall, the YARN panel, which combines Y-STR and Y-SNP genetic markers, meets forensic DNA quality assurance guidelines and holds potential for East Asian geographical origin inference and paternal lineage analysis.
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Affiliation(s)
- Haoliang Fan
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200433, China; School of Forensic Medicine, Shanxi Medical University, Taiyuan 030001, China.
| | - Yiran Xu
- Institute of Archaeological Science, Fudan University, Shanghai 200433, China.
| | - Yutao Zhao
- Public Security Bureau of Zhaoqing Municipality, Zhaoqing 526000, China.
| | - Kai Feng
- Duanzhou Branch of Zhaoqing Public Security Bureau, Zhaoqing 526060, China.
| | - Liuxi Hong
- Sihui Public Security Bureau of Guangdong Province, Zhaoqing 526299, China.
| | - Qiancheng Zhao
- Public Security Bureau of Zhaoqing Municipality, Zhaoqing 526000, China.
| | - Xiaoyu Lu
- Deepreads Biotech Company Limited, Guangzhou 510663, China.
| | - Meisen Shi
- Criminal Justice College of China University of Political Science and Law, Beijing 100088, China.
| | - Haiyan Li
- Criminal Technology Center of Guangdong Provincial Public Security Department, Guangzhou 510050, China.
| | - Lingxiang Wang
- MOE Laboratory for National Development and Intelligent Governance, Fudan University, Shanghai 200433, China.
| | - Shaoqing Wen
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200433, China; Institute of Archaeological Science, Fudan University, Shanghai 200433, China; MOE Laboratory for National Development and Intelligent Governance, Fudan University, Shanghai 200433, China.
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Du W, Zheng X, Jiang L, Li S, Lan S, Ye Y, Liu J. Forensic characteristics and genetic structure of the Chinese Tibetan population revealed by 38 X-chromosomal InDel loci. Forensic Sci Int 2024; 356:111961. [PMID: 38377671 DOI: 10.1016/j.forsciint.2024.111961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 01/04/2024] [Accepted: 02/04/2024] [Indexed: 02/22/2024]
Abstract
With the increasing importance of X-chromosome (Chr-X) genotyping in kinship identification, the exploitation of X chromosome genetic marker multiplex kits is increasing. The Human X-InDels amplification kit is a novel developed system which contained 38 X-chromosomal Insertion/deletion markers (X-InDels) and Amelogenin. Herein, we investigated the genetic diversity of the 38 X-InDels in the Tibetan ethnic minority (n = 792) from seven regions and evaluated the application potential of this novel panel. The rs16368 was the least variable locus, whereas the most polymorphic locus was the rs59605609 in Tibetan population. We confirmed three linkage groups with the haplotype diversities ranged from 0.5032 to 0.5976. The overall combined power of discrimination (PD) in males and females were 0.999999999582066 and 0.999999999999993, respectively. And the overall combined mean exclusion chance (MEC) values were not lower than 0.999125526990159. In addition, we explored the genetic relationships among the Tibetans in seven different regions via series of population comparison analyses, finding that the genetic relationship between the Ngari Tibetan and Chamdo Tibetan was the farthest, which was consistent with geographical distribution.
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Affiliation(s)
- Weian Du
- Key Laboratory of Evidence Science (China University of Political Science and Law), Ministry of Education, Beijing 100088, China; Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China; Guangdong Homy Genetics Incorporation, Foshan 528000, China
| | - Xinyue Zheng
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Lirong Jiang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Suyu Li
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Shengnan Lan
- Department of Forensic Toxicological Analysis, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Yi Ye
- Department of Forensic Toxicological Analysis, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China.
| | - Jing Liu
- Key Laboratory of Evidence Science (China University of Political Science and Law), Ministry of Education, Beijing 100088, China; Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China.
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Liu J, Li S, Su Y, Wen Y, Qin L, Zhao M, Hui M, Jiang L, Chen X, Hou Y, Wang Z. A proof-of-principle study: The potential application of MiniHap biomarkers in ancestry inference based on the QNome nanopore sequencing. Forensic Sci Int Genet 2024; 68:102947. [PMID: 37862770 DOI: 10.1016/j.fsigen.2023.102947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 09/25/2023] [Accepted: 10/16/2023] [Indexed: 10/22/2023]
Abstract
Haplotyped SNPs convey forensic-related information, and microhaplotypes (MHs), as the most representative of this kind of marker, have proved the potential value for human forensics. In recent years, nanopore sequencing technology has developed rapidly, with its outstanding ability to sequence long continuous DNA fragments and obtain phase information, making the detection of longer haplotype marker possible. In this proof-of-principle study, we proposed a new type of forensic marker, MiniHap, based on five or more SNPs within a molecular distance less than 800 bp, and investigated the haplotype data of 56 selected MiniHaps in five Chinese populations using the QNome nanopore sequencing. The sequencing performance, allele (haplotype) frequencies, forensic parameters, effective number of alleles (Ae), and informativeness (In) were subsequently calculated. In addition, we performed principal component analysis (PCA), phylogenetic tree, and structure analysis to investigate the population genetic relationships and ancestry components among the five investigated populations and 26 worldwide populations. MiniHap-04 exhibited remarkable forensic efficacy, with 148 haplotypes reported and the Ae was 66.9268. In addition, the power of discrimination (PD) was 0.9934, the probability of exclusion (PE) was 0.9898, and the In value was 0.7893. Of the 56 loci, 85.71% had PD values above 0.85, 66.07% had PE values above 0.54, 67.86% had Ae values over 7.0%, and 55.36% were with In values above 0.2 across all samples, indicating that most of the MiniHaps are suitable for individual identification, paternity testing, mixture deconvolution, and ancestry inference. Moreover, the results of PCA, phylogenetic tree and structure analysis demonstrated that this MiniHap panel had the competency in continental population ancestry inference, but the differentiation within intracontinental/linguistically restricted subpopulations was not ideal. Such findings suggested that the QNome device for MiniHap detection was feasible and this novel marker has the potential in ancestry inference. Yet, the establishment of a more comprehensive database with sufficient reference population data remains necessary to screen more suitable MiniHaps.
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Affiliation(s)
- Jing Liu
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Suyu Li
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Yonglin Su
- Department of Rehabilitation Medicine, West China Hospital Sichuan University, Chengdu 610041, China
| | - Yufeng Wen
- School of Life Sciences, Jilin University, Changchun 130012, China
| | - Liu Qin
- Qitan Technology Ltd., Chengdu 610044, China
| | - Mengyao Zhao
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Minxiao Hui
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Lirong Jiang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Xiacan Chen
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Yiping Hou
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Zheng Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China.
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Zhao GB, Miao L, Wang M, Yuan JH, Wei LH, Feng YS, Zhao J, Kang KL, Zhang C, Ji AQ, He G, Wang L. Developmental validation of a high-resolution panel genotyping 639 Y-chromosome SNP and InDel markers and its evolutionary features in Chinese populations. BMC Genomics 2023; 24:611. [PMID: 37828453 PMCID: PMC10568895 DOI: 10.1186/s12864-023-09709-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 10/02/2023] [Indexed: 10/14/2023] Open
Abstract
Uniparental-inherited haploid genetic marker of Y-chromosome single nucleotide polymorphisms (Y-SNP) have the power to provide a deep understanding of the human evolutionary past, forensic pedigree, and bio-geographical ancestry information. Several international cross-continental or regional Y-panels instead of Y-whole sequencing have recently been developed to promote Y-tools in forensic practice. However, panels based on next-generation sequencing (NGS) explicitly developed for Chinese populations are insufficient to represent the Chinese Y-chromosome genetic diversity and complex population structures, especially for Chinese-predominant haplogroup O. We developed and validated a 639-plex panel including 633 Y-SNPs and 6 Y-Insertion/deletions, which covered 573 Y haplogroups on the Y-DNA haplogroup tree. In this panel, subgroups from haplogroup O accounted for 64.4% of total inferable haplogroups. We reported the sequencing metrics of 354 libraries sequenced with this panel, with the average sequencing depth among 226 individuals being 3,741×. We illuminated the high level of concordance, accuracy, reproducibility, and specificity of the 639-plex panel and found that 610 loci were genotyped with as little as 0.03 ng of genomic DNA in the sensitivity test. 94.05% of the 639 loci were detectable in male-female mixed DNA samples with a mix ratio of 1:500. Nearly all of the loci were genotyped correctly when no more than 25 ng/μL tannic acid, 20 ng/μL humic acid, or 37.5 μM hematin was added to the amplification mixture. More than 80% of genotypes were obtained from degraded DNA samples with a degradation index of 11.76. Individuals from the same pedigree shared identical genotypes in 11 male pedigrees. Finally, we presented the complex evolutionary history of 183 northern Chinese Hans and six other Chinese populations, and found multiple founding lineages that contributed to the northern Han Chinese gene pool. The 639-plex panel proved an efficient tool for Chinese paternal studies and forensic applications.
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Affiliation(s)
- Guang-Bin Zhao
- National Engineering Laboratory for Forensic Science, Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China
| | - Lei Miao
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, China
| | - Mengge Wang
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510275, China
| | - Jia-Hui Yuan
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, China
| | - Lan-Hai Wei
- School of Ethnology and Anthropology, Inner Mongolia Normal University, Inner Mongolia, 010028, China
| | - Yao-Sen Feng
- National Engineering Laboratory for Forensic Science, Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China
| | - Jie Zhao
- National Engineering Laboratory for Forensic Science, Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China
| | - Ke-Lai Kang
- National Engineering Laboratory for Forensic Science, Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China
| | - Chi Zhang
- National Engineering Laboratory for Forensic Science, Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China
| | - An-Quan Ji
- National Engineering Laboratory for Forensic Science, Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China.
| | - Guanglin He
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610041, China.
| | - Le Wang
- National Engineering Laboratory for Forensic Science, Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China.
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, China.
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Li LY, Fan SG, Gong H, Fan X, Wang DC, Li NX, Jia FQ. Haplotype and Genetic Analysis of 41 Y-STR Loci in the Wuwei Han Population from Gansu Province, China. Curr Med Sci 2023; 43:184-190. [PMID: 36544037 DOI: 10.1007/s11596-022-2664-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 09/06/2022] [Indexed: 12/24/2022]
Abstract
OBJECTIVE Y-Chromosomal short tandem repeat polymorphism (Y-STR) analysis plays an indispensable role in the identification of male individuals, population genetics, and biogeographic research. While profiles of many populations based on Y-STR markers in human genomes are ample, haplotype data for the Wuwei Han are still scarce. METHODS In this study, 2180 unrelated Wuwei Han male individuals residing in Gansu Province, China were collected and genotyped using the novel Microreader™ 40Y Plus ID system. Phylogenetic relationship reconstructions, multidimensional scaling (MDS), and heatmap analysis were performed based on the genetic distance (Rst) values between our studied population and other populations of the Ymax module in the Y-STR Haplotype Reference Database (YHRD). RESULTS A total of 2129 unique haplotypes were obtained, and the haplotype diversity (HD) and discrimination capacity (DC) for the Wuwei Han were 0.9999 and 0.9931, respectively. CONCLUSION Our results demonstrate that the Wuwei Han population had intimate genetic relationships with East Asians, especially the geographically close Han populations. Overall, this Y-Chromosomal assay gives valuable information about paternal lineages in male individual tracking and genealogical database construction.
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Affiliation(s)
- Lu-Yao Li
- Department of Pathology, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China
| | - Sheng-Gui Fan
- The Judicial Authentication Center, Wuwei Public Security Bureau, Wuwei, 733000, China
| | - Hui Gong
- Department of Pathology, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China
| | - Xing Fan
- Department of Pathology, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China
| | - De-Chun Wang
- The Judicial Authentication Center, Wuwei Public Security Bureau, Wuwei, 733000, China
| | - Neng-Xiu Li
- The Judicial Authentication Center, Wuwei Public Security Bureau, Wuwei, 733000, China
| | - Fu-Quan Jia
- Department of Forensic Medicine, Inner Mongolia Medical University, Hohhot, 010059, China.
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Liu J, Jiang L, Zhao M, Du W, Wen Y, Li S, Zhang S, Fang F, Shen J, He G, Wang M, Dai H, Hou Y, Wang Z. Development and validation of a custom panel including 256 Y-SNPs for Chinese Y-chromosomal haplogroups dissection. Forensic Sci Int Genet 2022; 61:102786. [DOI: 10.1016/j.fsigen.2022.102786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 08/25/2022] [Accepted: 10/04/2022] [Indexed: 11/04/2022]
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Zhou Y, Cui W, Wu B, Zhu B. Development and validation of a new multiplex Y-STR panel designed to increase the power of discrimination. Electrophoresis 2022; 43:1899-1910. [PMID: 35856743 DOI: 10.1002/elps.202100313] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 03/28/2022] [Accepted: 07/08/2022] [Indexed: 12/14/2022]
Abstract
In an attempt to increase the discrimination capacity (DC) and reduce the adventitious match probability, a 6-dye multiplex Y-chromosomal short tandem repeat (Y-STR) panel named Y34plex was constructed that combined 25 Y-chromosomal markers (DYS456, DYS627, DYS390, DYS570, DYS635, DYS385a/b, DYS448, DYS437, DYS533, DYS449, DYS481, DYS392, DYS391, DYS389I, DYS460, YGATAH4, DYS438, DYS389II, DYS19, DYS458, DYF387S1a/b, DYS439, DYS393, DYS576, and DYS518) in widely used commercial kits, with nine highly polymorphic Y-STR loci (DYS557, DYS527a/b, DYS593, DYS444, DYS596, DYS643, DYS447, DYS549, and DYS645). The Y34plex is a promising type system to distinguish both unrelated and related male individuals due to the incorporation of rapidly mutated Y-STR loci. A validation study of the Y34plex was performed and followed the guidelines of the Scientific Working Group on DNA analysis methods. Results show that full Y-STR profiles were obtained from male/female DNA mixtures with 125 pg of male DNA in the presence of 50 ng of female DNA. The ability to tolerate polymerase chain reaction inhibitors commonly contained in forensic casework samples demonstrated the applicability and robustness of the Y34plex. Compared with the Yfiler Plus kit, the novel panel showed an increased power of discrimination in Chinese Wuxi Han population (n = 434). The overall haplotype diversity of the Y34plex was 0.999606, whereas DC value was 0.956221, which is suitable for use on forensic paternal investigation.
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Affiliation(s)
- Yongsong Zhou
- Shenzhen Stomatology Hospital (Pingshan), Southern Medical University, Shenzhen, P. R. China.,Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, P. R. China
| | - Wei Cui
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, P. R. China
| | - Buling Wu
- Shenzhen Stomatology Hospital (Pingshan), Southern Medical University, Shenzhen, P. R. China
| | - Bofeng Zhu
- Shenzhen Stomatology Hospital (Pingshan), Southern Medical University, Shenzhen, P. R. China.,Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, P. R. China.,Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, P. R. China
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Improving DNA Data Capacity: Forensic Parameters and Genetic Structure Analysis of Jinjiang Han Population with the Microreader™ Y Prime Plus ID System. Curr Med Sci 2022; 42:462-466. [PMID: 35403953 DOI: 10.1007/s11596-022-2570-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 11/01/2021] [Indexed: 12/14/2022]
Abstract
OBJECTIVE Population genetic analysis based on genetic markers harbors valuable forensic applications. In this regard, it is informative and imperative to explore Han groups as they are the largest population of China. In particular, there is a largely underrepresented amount of information from recent decades regarding the southeast costal Han Chinese. Therefore, the aim of this study is to investigate the available genetic characteristics of the Han population living in the Jinjiang, Fujian Province, Southeastern China. METHODS We sampled 858 saliva samples and used the commercially available Microreader™ Y Prime Plus ID System to identify population data of Y-short tandem repeat (STR) loci of this region. RESULTS A total of 822 different haplotypes were observed. The overall haplotype diversity, discriminatory power and haplotype match probability were 0.9999, 0.9999 and 0.0012, respectively. CONCLUSION Our results showed that the Jinjiang Han population was closely genetically related to Han groups of China. Overall, we identified a set of 37 Y-STRs that are highly polymorphic, and that can provide meaningful information in forensic practice and human genetic research.
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Zeng Y, Chen L, Wang M, Yang C, Liu H, Xiao C, Liu C, Li Y, Xu Q, Du W, Liu C. The Validation of a Single Multiplex Typing System With 45 Y-STR Markers for Familial Searching and Database Construction. Front Genet 2022; 13:842004. [PMID: 35154290 PMCID: PMC8829124 DOI: 10.3389/fgene.2022.842004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 01/07/2022] [Indexed: 11/13/2022] Open
Abstract
The Y-chromosomal short tandem repeat (Y-STR) is an effective forensic tool in familial searches and patrilineal relationship evaluation. However, currently available Y-STR panels often lack sufficient discriminatory power to resolve genetic relationships between distant relatives or within patrilocal populations. This study aims to establish a novel Y-STR amplification system for forensic casework analysis and database construction, which contains 44 slowly and moderately mutating and one rapidly mutating Y-STR. The validation of the assay was conducted following the recommendations of SWGDAM developmental validation guidelines. Different types of casework samples were tested and reliable profiles were obtained. Furthermore, we genotyped and analyzed 141 unrelated Han Chinese male samples. The results showed that this Y45 kit could improve the performance of identifying male individuals, higher haplotype diversity, and discrimination capacity when compared to the previous widely used Yfiler Plus kit. In general, the validation study demonstrated that the newly developed Y45 kit possesses high sensitivity, inhibitor tolerance, male specificity in a mixture, species specificity, and precision and is capable of forensic casework analysis and database construction.
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Affiliation(s)
- Ying Zeng
- School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Ling Chen
- School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Mengge Wang
- Guangzhou Forensic Science Institute, Guangzhou, China
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Chengliang Yang
- School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Hong Liu
- Guangzhou Forensic Science Institute, Guangzhou, China
| | - Cheng Xiao
- School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - ChangHui Liu
- Guangzhou Forensic Science Institute, Guangzhou, China
| | - Yue Li
- Guangzhou Forensic Science Institute, Guangzhou, China
| | - Quyi Xu
- Guangzhou Forensic Science Institute, Guangzhou, China
| | - Weian Du
- Guangdong Homy Genetics Incorporation, Foshan, China
| | - Chao Liu
- School of Forensic Medicine, Southern Medical University, Guangzhou, China
- Guangzhou Forensic Science Institute, Guangzhou, China
- *Correspondence: Chao Liu,
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Wang Z, Qin L, Liu J, Jiang L, Zou X, Chen X, Song F, Dai H, Hou Y. Forensic nanopore sequencing of microhaplotype markers using QitanTech's QNome. Forensic Sci Int Genet 2021; 57:102657. [PMID: 34973558 DOI: 10.1016/j.fsigen.2021.102657] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 12/22/2021] [Accepted: 12/23/2021] [Indexed: 12/20/2022]
Abstract
In recent years, extraordinary progress has been made in genome sequencing technologies, which has led to a decrease in cost and an increase in the diversity of sequenced genomes. Nanopore sequencing is one of the latest genome sequencing technologies. It aims to sequence longer contiguous pieces of DNA, which are essential for resolving structurally complex regions, and provides a new approach for forensic genetics to detect longer markers in real time. To date, multiple studies have been conducted to sequence forensic markers using MinION from Oxford Nanopore Technologies (ONT), and the results indicate that nanopore sequencing holds promise for forensic applications. Qitan Technology (QitanTech) recently launched its first commercial nanopore genome sequencer, QNome. It could achieve a read length of more than 150 kbp, and could generate approximately 500 Mb of data in 8 h. In this pilot study, we explored and validated this alternative nanopore sequencing device for microhaplotype (MH) profiling using a custom set of 15 MH loci. Seventy single-contributor samples were divided into 7 batches, each of which included 10 samples and control DNA 9947A and was sequenced by QNome. MH genotypes generated from QNome were compared to those from Ion Torrent sequencing (Ion S5XL system) to evaluate the accuracy and stability. Twelve samples randomly selected from the last three batches and Control DNA 9947A were also subjected to ONT MinION sequencing (with R9.4 flow cell) for parallel comparison. Based on MHtyper, a bioinformatics workflow developed for automated MH designation, all MH loci can be genotyped and reliably phased using the QNome data, with an overall accuracy of 99.83% (4 errors among 2310 genotypes). Three occurred near or in the region of homopolymer sequences, and one existed within 50 bp of the start of the sequencing reaction. In the last 15 samples (12 individual samples and 3 replicates of control DNA 9947A), two SNPs located at 4-mer homopolymers failed to obtain reliable genotypes on the MinION data. This study shows the potential of state-of-the-art nanopore sequencing methods to analyze forensic MH markers. Given the rapid pace of change, sporadic and nonrepetitive errors presented in this study are expected to be resolved by further developments of nanopore technologies and analysis tools.
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Affiliation(s)
- Zheng Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Liu Qin
- Qitan Technology Ltd., Chengdu 610044, China
| | - Jing Liu
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Lirong Jiang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Xing Zou
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Xiameng Chen
- Department of Forensic Pathology, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Feng Song
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Hao Dai
- Department of Forensic Pathology, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Yiping Hou
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China.
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